Help talk:Related

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The following text is copied from the MetaBase article in WikiPedia. I like it because its organized better than the content here... I need to rewrite the resources page!

Contents 1 Related Resources 2 Link dump 3 Second round (Return of the Linkdump) 4 Letter to 'BioWiki' practitioners ...

[edit] Related Resources

• The Molecular and Cellular Biology 'WikiProject', including;
  • Sequence alignment software
  • Software tools for molecular microscopy
• WikiData
• The Bioinformatics Links Directory features curated links to molecular resources, tools and databases.
• The Health Sciences Library System (HSLS) Online Bioinformatics Resources Collection (OBRC).
• The Molecular Biology Database Collection, a public on-line resource that lists the databases described in Nucleic Acids Research, together with other databases of value to the biologist.
• The Database of Biological Database (consists of 1200 Database entries covering wide range of databases useful for biological researchers).
• The Bioinformatics Links Directory
• EcoliWiki the goal for EcoliWiki is to generate community-based pages about everything related to E. coli K-12, its phages, plasmids, and mobile genetic elements.

[edit] Link dump

http://biowiki.net/index.php/All_the_BioWiki_contest_sites http://biome.info/index.php/Main_Page http://biopedia.org/index.php/Main_Page http://bioprograms.net/ http://biocafe.net/index.php/Main_Page http://biodenmark.org/index.php/Main_Page http://bioindonesia.org/index.php/Main_Page http://bioinformatist.org/index.php/Main_Page http://biolive.org/index.php/Main_Page http://biopicture.net/index.php/Main_Page http://biosingapore.org/index.php/Main_Page http://biostructure.org/index.php/Main_Page http://web.archive.org/web/20070302150127rn_1/biotip.org/index.php/Main_Page http://biovideo.org/index.php/Main_Page http://biozine.org/index.php/Main_Page http://contactome.org/index.php/Main_Page http://diseasepedia.net/index.php/Main_Page http://ethnome.org/index.php/Main_Page http://evolomics.net/index.php/Main_Page http://expressome.org/index.php/Main_Page http://introductome.org/index.php/Main_Page http://koreansnp.org/index.php/Main_Page http://mitogenome.org/index.php/Main_Page http://mybio.net/biowiki/Main_Page http://networkbiology.org/index.php/Main_Page http://pharmanome.org/index.php/Main_Page http://primatome.org/index.php/Main_Page http://stemcellbiology.net/index.php/Main_Page http://proteinfunction.net/index.php/Main_Page http://www.bioforge.net/forge/index.jspa http://tech.groups.yahoo.com/group/biohacking/ http://biowaredb.org/site/ http://kk.org/cooltools/archives/000582.php http://ecolihub.org/ http://en.wikibooks.org/wiki/Future/Biotechnology http://en.wikibooks.org/wiki/General_Biology/Genetics/Recombinant_DNA_Technology http://www.nexusresearchgroup.com/technical_data/carter.htm http://openwetware.org/wiki/Main_Page http://rsss.anu.edu.au/~janeth/home.html http://biohackery.com/ http://web.archive.org/web/20070420204234/http://www.dnahack.com/ http://biobricks.org/ (Endy just added some new mailing lists!)

Some other stuff.

http://openprosthetics.org/ http://obofoundry.org/ http://www.open-bio.org/wiki/Main_Page http://www.bioconductor.org/ http://www.openehr.org/home.html http://openeeg.sourceforge.net/ http://open-rtms.sourceforge.net/ http://transcenmentalism.org/OpenStim/tiki-index.php http://biocyc.org/open-compounds.shtml http://opendoar.org/ http://www.opensearch.org/Home http://www.howtoforge.com/ http://www.openhardwarefoundation.org/ http://www.ohloh.net/ http://www.earlham.edu/~peters/

-- Kanzure 04:53, 28 January 2008 (KST)

Oops. Do not forget

http://en.wikipedia.org/wiki/Synthetic_biology http://syntheticbiology.org/ http://www.syntheticgenomics.com/ http://heybryan.org/forums.html <-- the list of forums that I monitor (inc. many bio related sites) -- Kanzure 04:58, 28 January 2008 (KST)

http://bionumbers.org/ ( http://bionumbers.hms.harvard.edu/ )

What do we do with those ?? Should we create a categoy and start to order them ? --Pingou 00:27, 29 January 2008 (KST)

[edit] Second round (Return of the Linkdump)

Hey, I'd like to offer reactome.org and the following from the hplusroadmap wiki on computational biology:

• Compneurosci
  • Compartmental modeling
    • http://www.strout.net/conical/
    • http://www.cam.cornell.edu/~rclewley/cgi-bin/moin.cgi/
    • http://vlsi.eecs.harvard.edu/research/nans.html
    • http://retina.anatomy.upenn.edu/~rob/neuronc.html
    • http://snnap.uth.tmc.edu/
    • http://www.neurophys.biomedicale.univ-paris5.fr/~graham/surf-hippo.html
    • http://www.math.pitt.edu/~bard/xpp/xpp.html
  • Compneurosci db sites
    • http://www.cerebellum.org/
    • http://www.modelersworkspace.org/channeldb/ChannelDB.html
    • http://cocomac.org/home.asp
    • http://flybrain.neurobio.arizona.edu/
    • http://leonserver.bio.uci.edu//
    • http://microcircuit.epfl.ch/
    • http://neurodatabase.org/dataserver/goto.do;jsessionid=E1ADE2F4EC3DC76803174D9F1BDE361C?page=.home
    • http://www.neurobiologie.fu-berlin.de/beebrain/default.html
    • http://neurosys.cns.montana.edu/
  • Data acquisition and control
    • http://inls.ucsd.edu/~rpinto/dynclamp.html
    • http://www.neuro.gatech.edu/mrci/
    • http://inls.ucsd.edu/~nowotny/dynclamp.html
    • http://www.bu.edu/ndl/dynamicclamp.html
  • Data analysis and visualization
    • Time series data
      • http://datathief.org/
      • http://www.cam.cornell.edu/~rclewley/DSSRT.html
      • http://klustakwik.sourceforge.net/
      • http://klusters.sourceforge.net/
      • http://neuralc.sourceforge.net/
      • http://inls.ucsd.edu/~nowotny/neuranim.html
      • http://www.uoguelph.ca/~awillms/neurofit/
      • http://sourceforge.net/projects/neurofitter/
      • http://www.neuromatic.thinkrandom.com/
      • http://keck.ucsf.edu/projects/spiff/
      • http://millerlab.ucsf.edu/Software/Spiker/spiker.html
    • http://brainmap.wustl.edu/resources/caretnew.html
    • http://www.mssm.edu/cnic/tools-neurogl.html
    • http://www.mssm.edu/cnic/tools-ns.html
    • http://neuron.duke.edu/cells/usage.html
    • http://krasnow.gmu.edu/cn3/L-Neuron/index.htm
    • http://www.neugen.org/
    • http://www.rdg.ac.uk/neuromantic/
    • http://www.imagescience.org/meijering/software/neuronj/index.html
    • http://www.personal.soton.ac.uk/dales/morpho/
    • http://cns.iaf.cnrs-gif.fr/alain_demos.html#ntscable
  • Interoperability
    • http://brainml.org/goto.do;jsessionid=91425CAD140A7D8F8D3528DFA53012B4?page=.home
    • http://www.morphml.org/
    • http://www.neuralensemble.org/trac/PyNN/
    • http://www.neuroml.org/
  • Misc
    • http://www.neuroscholar.org/
  • Realistic network modeling
    • http://askja.bu.edu/catacomb/
    • http://compneuro.uwaterloo.ca/codelibrary/codelibrary.html#NESim
    • http://www.lsm.tugraz.at/csim/
    • http://www.kinness.net/
    • http://www.nest-initiative.org/index.php/Main_Page
    • http://www-sop.inria.fr/odyssee/software/mvaspike/
    • http://brain.cse.unr.edu/ncsDocs/
    • http://neuralsimulationlanguage.org/
    • http://www.physiol.ucl.ac.uk/research/silver_a/neuroConstruct/
    • http://www.cs.usfca.edu/neurosys/
    • http://sourceforge.net/projects/pcsim/
    • http://www.sccn.ucsd.edu/~arno/spikenet/
    • http://topographica.org/Home/index.html
    • http://sourceforge.net/projects/xnbc/
  • http://home.earthlink.net/~perlewitz/sftwr.html
  • http://www.copasi.org/tiki-index.php
  • http://128.125.37.80:8080/
  • http://www.qub.buffalo.edu/wiki/index.php/Main_Page
  • http://senselab.med.yale.edu/modeldb/
  • http://www.neurogems.org/
  • http://www.neuroml.org/index.html
  • http://senselab.med.yale.edu/NeuronDB/
  • http://neuron.duke.edu/
  • http://neurospaces.sourceforge.net/
  • http://www.psics.org/
  • http://www.ebi.ac.uk/compneur-srv/meredys.html
  • http://web.njit.edu/~matveev/calc.html
  • http://www.genesis-sim.org/GENESIS/
• Model databases
  • http://doqcs.ncbs.res.in/
• http://arep.med.harvard.edu/moma/
• http://x.amath.unc.edu:16080/BioNetS/
• http://www.chemengr.ucsb.edu/~ceweb/faculty/doyle/biosens/BioSens.htm
• http://biospice.sourceforge.net/
• http://biowarehouse.ai.sri.com/
• http://www.bioinformaticsservices.com/bis/resources/cybertext/IBcont.html
• http://www.cellml.org/
• http://discov.cs.kent.edu/resources/cell/cell_modeling.html
• http://biodynamics.indiana.edu/CellModeling/AboutCellX.html
• http://rtg.cis.upenn.edu/mobies/charon/
• http://www.dbi.tju.edu/tools/biospice/dbi_tju_feb_23/
• http://www.dbi.tju.edu/dbi/mod.php?mod=forum&menu=6
• http://dev.e-cell.org/
• http://arep.med.harvard.edu/gmc/fba.html
• http://www.ee.ucla.edu/~riccardo/GeneScreen/genescreen.html
• http://geneways.genomecenter.columbia.edu/
• http://www.gepasi.org/
• http://gfit.sourceforge.net/
• http://ftp.bioinformatics.org/pub/wrair/genecite/
• http://jdesigner.org/
• http://jigcell.biol.vt.edu/parameter.html
• http://jigcell.biol.vt.edu/index.html
• http://textmine.cu-genome.org/html/index.html
• http://biodynamics.indiana.edu/CellModeling/AboutKaryote.html
• http://receptor.seas.ucla.edu/lcDNA/
• http://www.mcell.psc.edu/
• http://www.mcell.cnl.salk.edu/
• http://monod.molsci.org/
• http://bioinformatics.nyu.edu/Projects/DARPA-BioComp/index.shtml
• http://bioinformatics.nyu.edu/Projects/Simpathica/
• http://oscill8.sourceforge.net/
• http://www.dbi.tju.edu/dbi/tools/paint/
• http://www.quantumii.com/qi/qisd2.html
• http://www.sbml.org/Forums/index.php?t=register&rid=0&reg_coppa=N
• http://icb.med.cornell.edu/crt/SigPath/DetailedInformation.xml
• http://www.cds.caltech.edu/sostools/
• http://www.ebi.ac.uk/~lenov/stochsim.html
• http://sbml.org/index.php/Main_Page
• http://www.sys-bio.org/

-- Kanzure 05:56, 16 March 2008 (KST)

[edit] Letter to 'BioWiki' practitioners ...

Something along these lines to be sent to each 'BioWiki' listed on the 'related resources' page. Also to be listed in the Nature Network 'BioWiki' group as a community hub for the BioWiki practitioners.

Dear 'BioWiki' practitioners,

nature network group - shared issues - shared goals - more communication.

Gathering information was the goal of MetaBase. For this reason information on BioWikis is particularly important... Please review your page in MetaBase.

No doubt there are other resouces that you know of that should be added to teh list on MetaBase...

Each page has been created with a minimum on content, namely, a short description, contact details and link to the homepage additionally at least one link has been provided to some other content of interest on your site.

Please review your pages entry in metabase.

Please

Please